Many fans of the Code Geass anime forget that there is actually a manga that came after the anime. Along with the manga series of R1 and R2, there are a number of other Code Geass manga based on other characters' perspectives of the story and alternate realities.
Even in the Code Geass: Lelouch of the Rebellion manga, there are a number of differences scattered throughout the story. Some are simple and minor changes like the absence of characters or changes in events, while others are pretty big to the atmosphere of the story in general, but it all generally follows the same basic story as the anime.
10 No Knightmares
One of the most prominent changes from the anime to the manga is the complete absence of the Knightmare frames. Knightmares are what all the characters in Code Geass use to fight one another, and what constitutes it as a mech anime.
The machines are piloted by a number of the characters, Lelouch, C.C., Kallen, and Suzaku to name a few. Many fans of the series have claimed that the absence of the Knightmares in the manga actually don't really have an impact on the story what so ever.
9 Comedy
The Code Geass manga is littered with comedic moments and sidebars that don't really match the serious tone of the anime. Of course, Lelouch always ran into silly situations, especially when it came to C.C. or anyone in the Student Council, but the comedy in the manga is different.
It is silly and cutesy, with adorable small sidebars that give readers an idea of what is going on in the characters' minds. Sometimes the sidebars consist of random characters interjecting their own opinions on what was happening. The manga felt like a true manga of the time, whereas the anime was way more intense throughout.
8 Chibi
The existence of chibi in the manga versus the anime is very similar to the idea of comedy being relevant as well. Chibi figures of the character seemed like were used in every silly scene in pretty much every early 2000s anime. It was as though chibi were the logo of anime, yet they were extremely absent in the Code Geass anime.
The manga used chibi a ton, of pretty much every character as well. Even the serious and stoic Lelouch gets his own chibi form.
7 Euphemia Appears Earlier
One of the minor differences in the manga is that Euphemia appears much earlier on in the series. Euphie attends Ashford, and Lelouch is able to meet her there in the story. Euphie has some of the most changes to her story.
Firstly, Cornelia isn't apart of the manga so Euphie does her own thing solo with Suzaku. Nina also isn't obsessed with Euphie in this iteration which saves a lot of drama that occurs later. Though Suzaku and Euphie were pretty romantic in the anime, they are even more so in the manga.
6 Events From Anime Are Rolled Together In Manga
Many of the events from the anime are rolled into each or changed for continuity purposes in the manga. The manga is much, much short than the anime series which has fifty episodes. The manga is about eight issues, with a little over 35 chapters.
Not only are chapters way shorter than episodes, but there is also overall just less content. Because of this, many of the major events were heavily focused on while others rolled into each other, meshing into one. Many of the minor events were also either scrapped completely or bled into the bigger events.
5 The Art Style
Most of the time in anime, the anime and manga share the same art style that becomes a staple of the series. However, with Code Geass, the art style of the anime and manga are actually different. In the anime, the characters are super angular and look incredibly long and slender, with pointed shoulders and corners.
The concept design was from CLAMP, the team behind Chobits and xxxHolic, so long fingers and limbs are excepted. However, the manga's art style has a much more cartoony feel to it and is a bit more generic than the anime.
4 The Length
As mentioned, the manga is way shorter than the anime. The anime sits at 50 episodes between two seasons, not including the films that retell the story, nor the newest movie Lelouch of the Re;surrection that continues and concludes the story of Lelouch and C.C.
The manga has eight volumes, with 38 chapters between the volumes. Five issues of the manga are based on R1 while the latter half is based on R2 and concludes at the same point in which the original anime concluded.
3 Different Perspectives
The interesting part of the Code Geass manga is that there is more than one. There is, of course, the base manga that retells the story of the anime called Lelouch of the Rebellion, which has been the main focus so far, but there are also others.
One of the manga, Code Geass: Suzaku of the Counterattack is actually based on the same story of the anime but is completely told from Suzaku's point of view. This manga has a lot more romance with Euphemia and dives into Suzaku's inner monologue while everything is going down. This manga is also only two issues long.
2 Nightmare of Nunnally
There are also manga based on alternate timelines. Code Geass: Nightmare of Nunnally is set in a different universe and follows a completely new story. In this manga, Lelouch disappears after he makes a deal with C.C. who leaves her doll, Nemo. Nemo and Nunnally make a contract with one another that grants Nunnally the power to fuse together and make a Knightmare battle suit. Overall, the story in this world is a lot more strange and complicated. C.C. killed Suzaku's father in order to save Lelouch and Nunnally, Lelouch and C.C. go missing for the greater part of the story.
Mao is in this story again, as well, but it seems like they just used the idea of a character attached to C.C. and kept the name as they totally changed everything about the character. Also, Euphemia lives, C.C. dies, and Lelouch inherits her Geass. It's a pretty nightmarish story and surprisingly runs for more than half as long as the original.
1 Alternate Timelines
There are also two short manga series filled with shorts called Code Geass Knight For Girls and Queen For Boys, which are pretty much just filled with fanservice. There are five of each of these mangas. Renya of Darkness is another Code Geass manga that acts as a prequel set in the Edo period of Japan, and OZ the Reflection which tells the story of two totally different protagonists.
And finally, in 2017 a new manga was released that is totally different than any of the other Code Geass stories. Code Geass: Lelouch the Tutor is a slice of life comedy and romance manga in which C.C. makes a contract with Lelouch stating that he will become her new tutor. This high school story is filled with a cute fluffy romance between the famous pairing and more sweet romance between Euphemia and Suzaku, without the worry of war or death around them.